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Persistent homology

Gard Spreemann, Benjamin Dunn, Magnus Bakke Botnan, Nils A Baas
We propose a method, based on persistent homology, to uncover topological properties of a priori unknown covariates in a system governed by the kinetic Ising model with time-varying external fields. As its starting point the method takes observations of the system under study, a list of suspected or known covariates, and observations of those covariates. We infer away the contributions of the suspected or known covariates, after which persistent homology reveals topological information about unknown remaining covariates...
March 2018: Physical Review. E
Jinha Yu, Antonella Ciancetta, Steven Dudas, Sierra Duca, Justine Lottermoser, Kenneth A Jacobson
The P2Y14 receptor (P2Y14 R) mediates inflammatory activity by activating neutrophil motility, but few classes of antagonists are known. We have explored the structure-activity relationship of a 3-(4-phenyl-1 H-1,2,3-triazol-1-yl)-5-(aryl)benzoic acid antagonist scaffold, assisted by docking and molecular dynamics (MD) simulation at a P2Y14 R homology model. A computational pipeline using the High Throughput MD Python environment guided the analogue design. Selection of candidates was based upon ligand-protein shape and complementarity and the persistence of ligand-protein interactions over time...
May 16, 2018: Journal of Medicinal Chemistry
Joseph J Wanford, Luke R Green, Jack Aidley, Christopher D Bayliss
Pathogenic Neisseria are responsible for significantly higher levels of morbidity and mortality than their commensal relatives despite having similar genetic contents. Neisseria possess a disparate arsenal of surface determinants that facilitate host colonisation and evasion of the immune response during persistent carriage. Adaptation to rapid changes in these hostile host environments is enabled by phase variation (PV) involving high frequency, stochastic switches in expression of surface determinants. In this study, we analysed 89 complete and 79 partial genomes, from the NCBI and Neisseria PubMLST databases, representative of multiple pathogenic and commensal species of Neisseria using PhasomeIt, a new program that identifies putatively phase-variable genes and homology groups by the presence of simple sequence repeats (SSR)...
2018: PloS One
Mokgadi Violet Gwangwa, Anna Margaretha Joubert, Michelle Helen Visagie
Tumourigenic tissue uses modified metabolic signalling pathways in order to support hyperproliferation and survival. Cancer-associated aerobic glycolysis resulting in lactic acid production was described nearly 100 years ago. Furthermore, increased reactive oxygen species (ROS) and lactate quantities increase metabolic, survival and proliferation signalling, resulting in increased tumourigenesis. In order to maintain redox balance, the cell possesses innate antioxidant defence systems such as superoxide dismutase, catalase and glutathione...
2018: Cellular & Molecular Biology Letters
Moo K Chung, Hyekyoung Lee, Victor Solo, Richard J Davidson, Seth D Pollak
Many existing brain network distances are based on matrix norms. The element-wise differences may fail to capture underlying topological differences. Further, matrix norms are sensitive to outliers. A few extreme edge weights may severely affect the distance. Thus it is necessary to develop network distances that recognize topology. In this paper, we introduce Gromov-Hausdorff (GH) and Kolmogorov-Smirnov (KS) distances. GH-distance is often used in persistent homology based brain network models. The superior performance of KS-distance is contrasted against matrix norms and GH-distance in random network simulations with the ground truths...
September 2017: Connectomics in neuroimaging: first International Workshop, CNI 2017, held in conjunction with MICCAI 2017, Quebec City, QC, Canada, September 14, 2017, Proceedings
Marie-Luise Zahno, Giuseppe Bertoni
(1) Background: Small ruminant lentiviruses (SRLV) persist in infected goats that mount a strong humoral immune response characterized by low neutralizing titers. In this study, we characterized the antibody response to SU5, a variable, immunodominant epitope of the envelope glycoprotein of SRLV. We tested the working hypothesis that the variability of SU5 reflects escape from neutralizing antibody. (2) Methods: Affinity purified anti-SU5 antibody were tested for their neutralizing activity to the homologous lentivirus...
May 2, 2018: Viruses
Kelin Xia
Despite the great advancement of experimental tools and theoretical models, a quantitative characterization of the microscopic structures of ion aggregates and their associated water hydrogen-bonding networks still remains a challenging problem. In this paper, a newly-invented mathematical method called persistent homology is introduced, for the first time, to quantitatively analyze the intrinsic topological properties of ion aggregation systems and hydrogen-bonding networks. The two most distinguishable properties of persistent homology analysis of assembly systems are as follows...
May 3, 2018: Physical Chemistry Chemical Physics: PCCP
Nicola Alessio, Tiziana Squillaro, Servet Özcan, Giovanni Di Bernardo, Massimo Venditti, Mariarosa Melone, Gianfranco Peluso, Umberto Galderisi
Mesenchymal stromal cells (MSCs) are not a homogenous population but comprehend several cell types, such as stem cells, progenitor cells, fibroblasts, and other types of cells. Among these is a population of pluripotent stem cells, which represent around 1-3% of MSCs. These cells, named multilineage-differentiating stress enduring (Muse) cells, are stress-tolerant cells. Stem cells may undergo several rounds of intrinsic and extrinsic stresses due to their long life and must have a robust and effective DNA damage checkpoint and DNA repair mechanism, which, following a genotoxic episode, promote the complete recovery of cells rather than triggering senescence and/or apoptosis...
April 10, 2018: Oncotarget
Bishnu Dawadi, Xinghong Wang, Rong Xiao, Abrar Muhammad, Youming Hou, Zhanghong Shi
Many notorious insect pests live in the symbiotic associations with gut microbiota. However, the mechanisms underlying how they host their gut microbiota are unknown. Most gut bacteria can release peptidoglycan (PGN) which is an important antigen to activate the immune response. Therefore, how to keep the appropriate gut immune intensity to host commensals while to efficiently remove enteropathogens is vital for insect health. This study is aimed at elucidating the roles of an amidase PGRP, Rf PGRP-LB, in maintaining the gut-microbe symbiosis of Red palm weevil (RPW), Rhynchophorus ferrugineus Olivier...
April 28, 2018: Developmental and Comparative Immunology
Julija Armalytė, Dukas Jurėnas, Renatas Krasauskas, Albinas Čepauskas, Edita Sužiedėlienė
Acinetobacter baumannii is one of the major causes of hard to treat multidrug-resistant hospital infections. A. baumannii features contributing to its spread and persistence in clinical environment are only beginning to be explored. Bacterial toxin-antitoxin (TA) systems are genetic loci shown to be involved in plasmid maintenance and proposed to function as components of stress response networks. Here we present a thorough characterization of type II system of A. baumannii , which is the most ubiquitous TA module present in A...
2018: Frontiers in Microbiology
Andrew Draganski, Moses T Tar, Guillermo Villegas, Joel M Friedman, Kelvin P Davies
BACKGROUND: Curcumin, a naturally occurring anti-inflammatory compound, has shown promise in pre-clinical studies to treat erectile dysfunction (ED) associated with type-1 diabetes. However, poor bioavailability following oral administration limits its efficacy. The present study evaluated the potential of topical application of curcumin-loaded nanoparticles (curc-np) to treat ED in a rat model of type-2 diabetes (T2D). AIM: Determine if topical application of curc-np treats ED in a T2D rat model and modulates expression of inflammatory markers...
May 2018: Journal of Sexual Medicine
Amreesh Parvez, Samir Giri, Gorkha Raj Giri, Monika Kumari, Renu Bisht, Priti Saxena
Mycobacterial pathogenesis is hallmarked by lipidic polyketides that decorate the cell envelope and mediate infection. However, factors mediating persistence remain largely unknown. Dynamic cell wall remodeling could facilitate the different pathogenic phases. Recent studies have implicated type III polyketide synthases (PKSs) in cell wall alterations in several bacteria. Comparative genome analysis revealed several type III pks gene clusters in mycobacteria. In this study, we report the functional characterization of two novel type III PKSs, MMAR_2470 and MMAR_2474, in Mycobacterium marinum...
April 25, 2018: Scientific Reports
Yasmin Gabay, Virginia M Weis, Simon K Davy
The genus Symbiodinium is physiologically diverse and so may differentially influence symbiosis establishment and function. To explore this, we inoculated aposymbiotic individuals of the sea anemone Exaiptasia pallida (commonly referred to as "Aiptasia"), a model for coral symbiosis, with one of five Symbiodinium species or types (S. microadriaticum, S. minutum, phylotype C3, S. trenchii, or S. voratum). The spatial pattern of colonization was monitored over time via confocal microscopy, and various physiological parameters were measured to assess symbiosis functionality...
February 2018: Biological Bulletin
Fuxiang Mao, Jihai Lei, Obeng Enoch, Ming Wei, Cui Zhao, Yanping Quan, Wei Yu
The domesticated silkworm is an ideal and economic insect model that plays crucial roles in sericulture and bioreactor. Bombyx mori nucleopolyhedrovirus (BmNPV) is not only an infectious pathogen to B. mori, but also an efficient vector expressing recombinant proteins. Although, the proteomics of silkworm and BmN cell membrane lipid raft towards BmNPV infection had been investigated, proteome results of BmN cells upon BmNPV challenge currently remain ambiguous. In order to explore the interaction between silkworm and BmNPV, we analyzed several pivotal processes of BmNPV infected BmN cell by quantitative mass spectrometry...
April 16, 2018: Journal of Proteomics
Jennifer M Reiman, Sanjai Kumar, Ingrid B Rodriguez, Sedami Gnidehou, Koichi Ito, Danielle I Stanisic, Moses Lee, Virginia McPhun, Victoria Majam, Nicole M Willemsen, Michael R Batzloff, Amber I Raja, Brad Dooley, Stephen L Hoffman, Stephanie K Yanow, Michael F Good
Objectives: Blood stage malaria parasites attenuated with seco-cyclopropyl pyrrolo indole (CPI) analogues induce robust immunity in mice to homologous and heterologous malaria parasites and are being considered for the development of a human vaccine. However, it is not understood how attenuated parasites induce immunity. We showed that following vaccination, parasite DNA persisted in blood for several months, raising the possibility that ongoing immune stimulation may be critical. However, parasites were not seen microscopically beyond 24 h postvaccination...
2018: Clinical & Translational Immunology
Shahar Biechonski, Leonid Olender, Adi Zipin-Roitman, Muhammad Yassin, Nasma Aqaqe, Victoria Marcu-Malina, Melanie Rall-Scharpf, Magan Trottier, M Stephen Meyn, Lisa Wiesmüller, Katia Beider, Yael Raz, Dan Grisaru, Arnon Nagler, Michael Milyavsky
Failure to precisely repair DNA damage in self-renewing Hematopoietic Stem and early Progenitor Cells (HSPCs) can disrupt normal hematopoiesis and promote leukemogenesis. Although HSPCs are widely considered a target of ionizing radiation (IR)-induced hematopoietic injury, definitive data regarding cell death, DNA repair, and genomic stability in these rare quiescent cells are scarce. We found that irradiated HSPCs, but not lineage-committed progenitors (CPs), undergo rapid ATM-dependent apoptosis, which is suppressed upon interaction with bone-marrow stroma cells...
April 17, 2018: Scientific Reports
Sergi Torres-Puig, Carlos Martínez-Torró, Ignasi Granero-Moya, Enrique Querol, Jaume Piñol, Oscar Q Pich
In the human pathogen Mycoplasma genitalium, homologous recombination is under the control of σ20, an alternative sigma factor that boosts the generation of genetic and antigenic diversity in the population. Under laboratory growth conditions, σ20 activation is rare and the factors governing its intermittent activity are unknown. Two σ20-regulated genes, rrlA and rrlB, showed to be important for recombination of homologous DNA sequences in this bacterium. Herein, we demonstrate that rrlA and rrlB code for two small proteins that participate in a feed-forward loop essential for σ20 function...
April 11, 2018: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
Sarang Tartey, Prajwal Gurung, Tejasvi Krishna Dasari, Amanda Burton, Thirumala-Devi Kanneganti
Mice homozygous for the Tyr208Asn amino acid substitution in the carboxy terminus of Src homology region 2 (SH2) domain-containing phosphatase 1 (SHP-1) (referred to as Ptpn6spin mice) spontaneously develop a severe inflammatory disease resembling neutrophilic dermatosis in humans. Disease in Ptpn6spin mice is characterized by persistent footpad swelling and suppurative inflammation. Recently, in addition to IL-1α and IL-1R signaling, we demonstrated a pivotal role for several kinases such as SYK, RIPK1, and TAK1 in promoting inflammatory disease in Ptpn6spin mice...
April 9, 2018: Journal of Clinical Investigation
Bomyi Lim, Tyler Heist, Michael Levine, Takashi Fukaya
How remote enhancers interact with appropriate target genes persists as a central mystery in gene regulation. Here, we exploit the properties of transvection to explore enhancer-promoter communication between homologous chromosomes in living Drosophila embryos. We successfully visualized the activation of an MS2-tagged reporter gene by a defined developmental enhancer located in trans on the other homolog. This trans-homolog activation depends on insulator DNAs, which increase the stability-but not the frequency-of homolog pairing...
March 23, 2018: Molecular Cell
Karuvelan Murugan, Namasivayam Vasudevan
Polychlorinated biphenyls (PCBs) are xenobiotic compounds that persists in the environment for long-term, though its productivity is banned. Abatement of the pollutants have become laborious due to it's recalcitrant nature in the environment leading to toxic effects in humans and other living beings. Biphenyl degrading bacteria co-metabolically degrade low chlorinated PCBs using the active metabolic pathway. bph operon possess different genetic arrangements in gram positive and gram negative bacteria. The binding ability of the genes and the active sites were determined by PCB docking studies...
March 29, 2018: Ecotoxicology and Environmental Safety
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